Task #4114 (closed)
Opened 13 years ago
Closed 11 years ago
Better support for N-dimensional data
Reported by: | crueden-x | Owned by: | mhiner-x |
---|---|---|---|
Priority: | major | Milestone: | Unscheduled |
Component: | Bio-Formats | Version: | 4.4.8 |
Keywords: | n.a. | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by crueden-x)
Eliminate IFormatReader.getChannelDimTypes and IFormatReader.getChannelDimLengths, in favor of more comprehensive getDimTypes and getDimLengths methods, which return all used dimensions in correct rasterization order.
- OME dimensions include: X, Y, Z, C, T
- Examples of non-OME dimensions:
- lifetime bins
- excitation wavelength
- polarization
- screen
- plate
- well
- field
Advantages:
- fully capable of expressing N-dimensional image data
- allows for XZ scans and other spatial configurations
- eliminates the need for DimensionOrder? and Interleaved core metadata
Work to do:
- Rework ChannelSeparator? a little
- It should always "pull" XY to the front
- Rework DimensionSwapper?; it is more complex now
- Rework DataBrowser? to use new methods, displaying extra sliders as before
- Rework FileStitcher? and AxisGuesser? a bit
- Guessed axes become new dimensions
- Change anywhere else that calls getChannelDim* methods
- InCell? reader can be retrofitted to use this new functionality
- Certain other readers can benefit as well: Flex, Fluoview, ...
- Initially, conversion to OME-TIFF with bfconvert should throw an exception if any dimensions beyond 5D exist, since there is nowhere in the OME-XML schema to store the extra dimensional information
Change History (4)
comment:1 Changed 13 years ago by jmoore
comment:2 Changed 13 years ago by crueden-x
- Description modified (diff)
- Owner changed from curtis to crueden-x
- Reporter changed from curtis to crueden-x
comment:3 Changed 12 years ago by crueden-x
- Milestone changed from OMERO-Beta4.4 to Unscheduled
- Owner changed from crueden-x to mhiner-x
This work fits in well with our SCIFIO efforts. Added to SCIFIO core refactoring story.
comment:4 Changed 11 years ago by mhiner-x
- Resolution set to duplicate
- Status changed from new to closed
- Version set to 4.4.8
Moved to github under SCIFIO issues.
imported from bio-formats:#398